You said, ...push multiple key-value pairs onto an existing hash. Just to clarify, values (scalars) are pushed onto an array; you don't push onto a hash.

The push in your while loop adds array references as values associated with keys, so you see a mix of data from the Dumper output (your push @{$gene{$key}}, $value; notation says treat the key's associated value as an array and push the contents of $value onto that array):